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@ARTICLE{BERN2000,
  author = {Simon Bern{\`e}che and Benoit Roux},
  title = {Molecular Dynamics of the {KcsA} {K$^+$} channel in a bilayer membrane},
  journal = BJ,
  year = {2000},
  volume = {78},
  pages = {2900--2917},
  number = {6}
}

@ARTICLE{SkIz02,
  author = {R.~D. Skeel and J.~A. Izaguirre},
  title = {An Impulse Integrator for {L}angevin Dynamics},
  journal = MP,
  year = {2002},
  volume = {100},
  pages = {3885--3891},
  number = {24}
}

@Article{MaFV06,
        author = {L.~Maragliano and A.~Fisher and E.~Vanden-Eijnden},
        title = {String method in collective variables: Minimum free energy
paths and iscommittor surfaces},
        year = {2006},
        journal = JCP,
        volume = 125,
        pages = {024106}
}

@Article{LaPa02,
  author = {A.~Laio and M.~Parinello},
  title = {Escaping free energy minima},
  year = {2002},
  journal = PNAS,
  volume = 99,
  pages = {12562-12566}
}

@ARTICLE{BCDG02,
  author = {P.~G.~Bolhuis and D.~Chandler and C.~Dellago and P.~L.~Geissler},
  title = {Transition Path Sampling: Throwing ropes over rough mountain passes,
        in the dark},
  journal = ARBBC,
  year = {2002},
  volume = {53},
  pages = {291--318}
}

@Article{WeRV02,
        author = {W.~E and W.~Ren and E.~Vanden-Eijnden},
        title = {String method for the study of rare events},
        year = {2002},
        journal = PRB,
        volume = 66,
        pages = {052301}
}

@ARTICLE{DeBG02,
  author = {C. Dellago and P.~G.Bolhuis and P.~L. Geissler},
  title = {Transition Path Sampling},
  journal = ACP,
  year = {2002},
  number = {123},
  pages = {1585-1595}
}

@ARTICLE{ErBo05,
  author = {Titus S. Van Erp and Peter G. Bolhuis},
  title = {Elaborating Transition Interface Sampling Methods},
  journal = jcmp,
  year = {2005},
  volume = {205},
  pages = {157--181}
}


@Article{SPPI08,
    author = {Christopher R. Sweet and Paula Petrone and Vijay S. Pande and Jes\'{u}s A. Izaguirre},
    title = {Normal mode partitioning of {L}angevin dynamics for biomolecules},
    year = {2008},
    journal = JCP,
    volume = 128,
    issue = 11,
    pages = {1--14},
}

@ARTICLE{TamS01,
  author = {F.~Tama and Y.~H.~Sanejouand},
  title = {Conformational changes of proteins arising from normal mode calculations},
  journal = PE,
  year = {2001},
  volume = {14},
  pages = {1-6},
  number = {1}
}

@Article{LeSS85,
        author = {M.~Levitt and C.~Sander and P.~S.~Stern},
        title = {Protein normal-mode dynamics : trypsin inhibitor, crambin, ribonuclease and lysozyme},
        year = {1985},
        journal = JMB,
        volume = 181,
        pages = {423-447}
}

@ARTICLE{TORR77,
  author = {G.~M.~Torrie and S.~P.~Valleau},
  title = {Nonphysical sampling distributions in {M}onte {C}arlo free-energy
        estimation: Umbrella Sampling},
  journal = JCMP,
  year = {1977},
  volume = {23},
  pages = {187--199}
}



@ARTICLE{DaWP02,
  author = {Eric Darve and Michael A. Wilson and Andrew Pohorille},
  title = {Calculating Free Energies Using a Scaled-Force Molecular Dynamics Algorithm},
  journal = MS,
  year = {2002},
  volume = {28},
  pages = {113}
}

@ARTICLE{Bolh03,
  author = {P.~Bolhuis},
  title = {Transition path sampling of ${\beta}$-hairpin peptide},
  journal = PNAS,
  year = {2003},
  volume = {100},
  pages = {12129-12134},
  number = {21}
}

@ARTICLE{Elbe05,
  author = {R. Elber},
  title = {Long-timescale simulation methods},
  journal = COSB,
  year = {2005},
  volume = {15},
  pages = {151--156}
}

@ARTICLE{PePa06,
  author = {P.~Petrone and V.~Pande},
  title = {Can Conformational Change be described by only a few normal modes?},
  journal = BJ,
  year = {2006},
  volume = {90},
  pages = {1583-1593}
}



@ARTICLE{RoAT05,
  author = {Lula Rosso and Jerry B. Abrams and Mark E. Tuckerman},
  title = {Mapping the Backbone Dihedral Free-Energy Surfaces in Small Peptides
        in Solution Using Adiabatic Free-Energy Dynamics},
  journal = JPCB,
  year = {2005},
  volume = {109},
  pages = {4162--4167}
}


@INPROCEEDINGS{CiSI07,
  author = {Trevor Cickovski and Chris Sweet and Jes\'{u}s A.\ Izaguirre},
  title = {{MDL,} {A} Domain-Specific Language for Molecular Dynamics},
  booktitle = {Proc. 40th Annual Simulation Symposium},
  year = {2007}
}


@Article{MarV07,
    author = {L.~Maragliano and E.~Vanden-Eijnden},
    title = {On-the-fly string method for minimum free energy path calculations},
    year = {2007},
    journal = CPL,
    volume = 446,
    pages = {182-190}
}

@Article{WeRV07,
   author = {W.~E and W.~Ren and E.~Vanden-Eijnden},
   title = {Simplified and improved string method for computing the minimum free energy
        in barrier-crossing paths},
   year = {2007},
   journal = JCP,
   volume = 126,
   pages = {164103}
}


@Article{PaSR08,
  author = {Albert C.~Pan and D.~Sezer and B.~Roux},
  title = {Finding Transition Pathways Using String Method with Swarms of Trajectories},
  year = {2008},
  journal = JPCB,
  volume = 112,
  number = 11,
  pages = {3432-3440}
}

@Article{SheF05,
   author = {Min-Yi Shen and K.~F.~Freed},
   title = {A simple method for faster nonbonded force evaluations},
   year = {2005},
   journal = JCC,
   volume = 26,
   pages = {691-698}
}

@Article{HeUJ00,
   author = {G.~Henkelman and B.~P.~Uberuaga and H.~J\'{o}nsson},
   title = {A climbing image nudged elastic band method for finding saddle points and minimum energy paths},
   year = {2000},
   journal = JCP,
   volume = 113,
   number = 22,
   pages = {9901-9904}
}

@Article{WeES07,
   author = {Anthony M.~A.~West and Ron Elber and David Shalloway},
   title = {Extending molecular dynamics timescales with milestoning : Example of complex kinetics in a solvated peptide},
   year = {2007},
   journal = JCP,
   volume = 126,
   pages = {145104}
}

@Article{MiVC07,
   author = {Thomas F. Miller III and Eric Vanden-Eijnden and David Chandler},
   title = {Solvent coarse-graining and the String Method applied to the Hydrophobic collapse of a hydrated chain},
   year = {2007},
   journal = PNAS,
   volume = 104,
   number = 37,
   pages = {14559-14564}

}

@INPROCEEDINGS{IzSw09,
   author = {Jes\'{u}s A.~Izaguirre and Christopher R.~ Sweet},
   title = {Adaptive dimensionality reduction of stochastic differential equations for protein dynamics},
   booktitle = {Proc.~Second International Workshop on Model Reduction in Reacting Flows},
   year = {2009},
   annote = {Preprint: \url{http://www.nd.edu/~izaguirr/papers/modelreduction.pdf}}
}

@ARTICLE{MACK92,
  author = {A. D. {MacKerell Jr.} and D. Bashford and M. Bellott and R. L. {Dunbrack
        Jr.} and J. Evanseck and M. J. Field and S. Fischer and J. Gao and
        H. Guo and S. Ha and D. Joseph and L. Kuchnir and K. Kuczera and
        F. T. K. Lau and C. Mattos and S. Michnick and T. Ngo and D. T. Nguyen
        and B. Prodhom and B. Roux and M. Schlenkrich and J. Smith and R.
        Stote and J. Straub and M. Watanabe and J. {Wiorkiewicz-Kuczera}
        and D. Yin and M. Karplus},
  title = {Self-consistent parameterization of biomolecules for molecular modeling
        and condensed phase simulations},
  journal = FASEB,
  year = {1992},
  volume = {A143},
  pages = {6},
}

@ARTICLE{MACK98,
  author = {A. D. {MacKerell Jr.} and D. Bashford and M. Bellott and R. L. {Dunbrack
        Jr.} and J. Evanseck and M. J. Field and S. Fischer and J. Gao and
        H. Guo and S. Ha and D. Joseph and L. Kuchnir and K. Kuczera and
        F. T. K. Lau and C. Mattos and S. Michnick and T. Ngo and D. T. Nguyen
        and B. Prodhom and I. W. E. Reiher and B. Roux and M. Schlenkrich
        and J. Smith and R. Stote and J. Straub and M. Watanabe and J. {Wiorkiewicz-Kuczera}
        and D. Yin and M. Karplus},
  title = {All-hydrogen empirical potential for molecular modeling and dynamics
        studies of proteins using the {CHARMM22} force field.},
  journal = JPCB,
  year = {1998},
  volume = {102},
  pages = {3586--3616},
}

@INPROCEEDINGS{IzSP10,
  author = {Jes\'{u}s A.~Izaguirre and Christopher R.~ Sweet and Vijay Pande},
  title = {Multiscale dynamics of macromolecules using Normal Mode Langevin},
  booktitle = {Pacific Symposium on Bioinformatics (PSB 2010)},
  year = {2010},
  volume = 15,
  pages = {240-51}
}

@Article{MaVa06,
   author = {L.~Maragliano and E.~Vanden-Eijnden},
   title = {A temperature accelerated method for sampling free energy and determining
     reaction pathways in rare event simulations},
   year = {2006},
   journal = CPL,
   volume = 426,
   pages = {168-175}
}

@Article{PHBC04,
   author = {Baron Peters and Andreas Heyden and Alexis T. Bell and Arup Chakraborty},
   title = {A growing String method for determining transition states : Comparison to the nudged elastic band and other methods},
   year = {2004},
   journal = JCP,
   volume = 120,
   number = 17,
   pages = {7877-7887}
}

@Article{BurY06,
   author = {Steven K. Burger and Weitao Yang},
   title = {Quadratic string method for determining the minimum-energy path based on multiobjective optimization},
   year = {2006},
   journal = JCP,
   volume = 124,
   number = 19,
   pages = {054109}
}

@Article{MoGB08,
   author = {Antoni Aguilar-Morgas and Xavier Gim\'{e}nez and Josep Maria Bofill},
   title = {Finding reaction paths using the potential energy as reaction coordinate},
   year = {2008},
   journal = JCP,
   volume = 128,
   pages = {104102}
}

@Article{GoBH08,
   author = {Anthony Goodrow and Alexis T. Bell and Martin Head-Gordon},
   title = {Development and application of a hybrid method involving interpolation and ab initio calculations
       for the determination of transition states},
   year = {2008},
   journal = JCP,
   volume = 129,
   pages = {174109}

}

@ARTICLE{Matt04,
  author = {Thierry Matthey and Trevor Cickovski and Scott~S. Hampton and Alice
        Ko and Qun Ma and Matthew Nyerges and Troy Raeder and Thomas Slabach
        and Jes\'{u}s A. Izaguirre},
  title = {\textsc{{P}roto{M}ol}: {A}n Object-Oriented Framework for Prototyping
        Novel Algorithms for Molecular Dynamics},
  journal = ACMTMS,
  year = {2004},
  volume = {30},
  pages = {237--265},
  number = {3}
}

@INPROCEEDINGS{MaIz01,
  author = {T. Matthey and J.~A. Izaguirre},
  title = {Proto{M}ol: A Molecular Dynamics Framework with Incremental Parallelization},
  booktitle = {Proc. of the Tenth SIAM Conf. on Parallel Processing for Scientific
        Computing (PP01)},
  year = {2001},
  series = {Proceedings in Applied Mathematics},
  address = {Philadelphia},
  month = MAR,
  publisher = {Society for Industrial and Applied Mathematics},
  note = {Preprint: \url{http://www.nd.edu/~izaguirr/papers/proto.pdf}}
}

@ARTICLE{EGCS03,
  author = {R.~Elber and A.~Ghosh and A.~Cardenas and H.~Stern},
  title = {Bridging the gap between reaction pathways, long time dynamics and
        calculation of rates},
  journal = ACP,
  year = {2003},
  volume = {126},
  pages = {93-129}
}

@Article{ElGC02,
  author = {R.~Elber and A.~Ghosh and A.~Cardenas},
  title = {Long Time Dynamics of Complex Systems},
  journal = ACR,
  year = {2002},
  volume = 35,
  pages = {396-403}
}

@ARTICLE{FarE04,
  author = {A.~K.~Faradjian and R.~Elber},
  title = {Computing time scales from reaction coordinates by milestoning},
  journal = JCP,
  year = {2004},
  volume = {120},
  pages = {10880-10889},
  number = {23}
}

@Article{Cick09,
  author = {Trevor Cickovski and Santanu Chatterjee and Jacob Wenger and Chris Sweet and Jes\'{u}s A. Izaguirre},
  title = {MDLab : A Molecular Dynamics Simulation Prototyping Environment},
  journal = JCC,
  year = {2009},
  volume = {30},
  pages = {1000}
}

@BOOK{Schl02,
  title = {Molecular Modeling and Simulation - An Interdisciplinary Guide},
  publisher = {Springer-Verlag},
  year = {2002},
  author = {Tamar Schlick},
  address = {New York, NY},
  remark = {ISBN: 0-387-95404-X}
}

@Article{ZhCY09,
  author = {L.~Zheng and M.~Chen and W.~Yang},
  title = {Simultaneous escaping of explicit and hidden free energy barriers : Application of the orthogonal space random walk strategy in generalized ensemble based conformational sampling},
  journal = JCP,
  year = {2009},
  volume = {130},
  number = {10},
  pages = {234105},
}

@Article{BrHC09,
  author = {Jason B.~Brokaw and Kevin R.~Haas and Jhih-Wei Chu},
  title = {Reaction path optimization with Holonomic constraints and kinetic energy potential},
  journal = JCTC,
  year = 2009,
  volume = {5},
  pages = {2050-2061}
}

@ARTICLE{BaSc98b,
  author = {Eric Barth and Tamar Schlick},
  title = {Extrapolation Versus Impulse in Multiple-Timestepping Schemes. {II}.
        {L}inear Analysis and Applications to {N}ewtonian and {L}angevin
        Dynamics},
  journal = {J. Chem.\ Phys.},
  year = {1998},
  volume = {109},
  pages = {1633--1642},
  number = {5}
}

@ARTICLE{FLZB97,
  author = {Fransisco Figueirido and Ronald M. Levy and Ruhong Zhou and Bruce
        J. Berne},
  title = {Large Scale Simulation of Macromolecules in Solution: Combining the
        Periodic Fast Multipole Method with Multiple Time Step Integrators},
  journal = {J. Chem.\ Phys.},
  year = {1997},
  volume = {106},
  pages = {9835--9849},
  number = {23}
}

@ARTICLE{WaKa95,
  author = {Masakatsu Watanabe and Martin Karplus},
  title = {Simulation of Macromolecules by Multiple-Time-Step Methods},
  journal = {J. Phys.\ Chem.},
  year = {1995},
  volume = {99},
  pages = {5680--5697},
  number = {15},
  nabstract = {Molecular dynamics simulations of macromolecules require long computation
        times to generate the trajectories needed for determining their thermodynamic
        and dynamic properties. The most rapidly varying quantities, such
        as the bond lengths, limit the integration time step, while the more
        slowly varying molecular processes are of primary interest. The form
        of the empirical potential energy function used in simulations of
        macromolecules makes it possible to exploit the existing separation
        of time scales by use of the reversible multiple time-step method
        (Tuckerman, Berne, and Martyna. J. Chem. Phys. 1992, 97, 1990). Implementation
        of the method in Cartesian coordinates yields an efficient multiple
        time-step algorithm for molecular dynamics with a velocity Verlet
        integrator. The forces acting on individual atoms are classified
        as hard, medium, and soft; for example, hard forces are contributed
        by bond-stretching and bond-angle bending terms, medium forces by
        dihedral angle and nonbonded (van der Waals and electrostatic) interaction
        terms acting on hydrogen atoms, and soft forces by the remaining
        nonbonded interaction terms. The multiple time-step approach is tested
        in short (10 ps) simulations of the pentapeptide Met-enkephalin and
        the protein the bovine pancreatic trypsin inhibitor. The stability
        of the integration methods and the dynamics and structural results
        are compared with those obtained with standard single time-step methods,
        with and without SHAKE. The results demonstrate that, for peptides
        and proteins, the multiple time-step method yields stable trajectories
        with a saving of up to a factors of 4 in computer time. Some properties
        (e.g., relaxation times, hydrogen bonding characteristics) are given
        accurately in short simulations (10 ps) even from unstable integrators
        with large time steps. A series of longer simulations (100 ps) of
        BPTI confirm many of the results found in the shorter simulations.
        However, some larger differences in behavior result from the use
        of less stable integration algorithms; in one case, the simulation
        diverges. Also, use of the SHAKE algorithm for a hydrogen atoms containing
        bonds with a stable integrator is shown to affect some properties
        of the system (e.g., the spectral densities associated with the main
        chain and side chain torsional motions). The sensitivity appears
        to arise from the large number of hydrogen atoms in proteins and
        from the densely packed nature of the structures. Thus, a detailed
        treatment of the hydrogen atoms, including their bond length fluctuations,
        appears to be important for obtaining highly accurate dynamics of
        proteins.}
}

@ARTICLE{MaIz03a,
  author = {Q.\ Ma and J.~A.\ Izaguirre},
  title = {Targeted Mollified Impulse --- a Multiscale Stochastic Integrator
        for Long Molecular Dynamics Simulations},
  journal = MMS,
  year = {2003},
  volume = {2},
  pages = {1--21},
  number = {1}
}

@ARTICLE{CRYB05,
  author = {C.~Chennubhotla and A.~J.~Rader and L.~Yang and I.~Bahar},
  title = {Elastic Network models for understanding biomolecular machinery:from
        enzymes to supramolecular assemblies},
  journal = PHCB,
  year = {2005},
  volume = {2},
  pages = {S173-S180}
}


